U.S. patent application number 17/578498 was filed with the patent office on 2022-08-04 for optimal selection method of gene chip probes for cancer screening.
The applicant listed for this patent is BEIJING BIONAXIN BIOTECH CO., LTD. Invention is credited to ZIANG HUA, NA LI, BAOQUAN LIU, JUNXING WAN, JIAN ZHANG, MEIYING ZHU, TIAN ZHU.
Application Number | 20220246237 17/578498 |
Document ID | / |
Family ID | |
Filed Date | 2022-08-04 |
United States Patent
Application |
20220246237 |
Kind Code |
A1 |
HUA; ZIANG ; et al. |
August 4, 2022 |
OPTIMAL SELECTION METHOD OF GENE CHIP PROBES FOR CANCER
SCREENING
Abstract
The invention relates to an optimal selection method of gene
chip probes for cancer screening. The method is characterized in
that the gene chip probes capable of being used for cancer
screening are obtained through three stages of constructing a point
mutation site (SNV) group, constructing a candidate probe group and
verifying and confirming probes on the basis of nucleic acid data
of a confirmed case of a selected cancer.
Inventors: |
HUA; ZIANG; (BEIJING,
CN) ; LIU; BAOQUAN; (BEIJING, CN) ; ZHU;
TIAN; (BEIJING, CN) ; ZHU; MEIYING; (BEIJING,
CN) ; WAN; JUNXING; (BEIJING, CN) ; ZHANG;
JIAN; (BEIJING, CN) ; LI; NA; (BEIJING,
CN) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
BEIJING BIONAXIN BIOTECH CO., LTD |
BEIJING |
|
CN |
|
|
Appl. No.: |
17/578498 |
Filed: |
January 19, 2022 |
International
Class: |
G16B 25/20 20060101
G16B025/20; C12Q 1/6811 20060101 C12Q001/6811; C12Q 1/6886 20060101
C12Q001/6886 |
Foreign Application Data
Date |
Code |
Application Number |
Feb 1, 2021 |
CN |
2021101334813 |
Claims
1. An optimal selection method of gene chip probes for cancer
screening characterized in comprising the following steps: S1
Selecting a cancer as the screening target and obtaining nucleic
acid detection data of confirmed cases of the cancer; S2
Determining corresponding point mutation sites (SNV) and
constructing a point mutation site (SNV) group by sequence
alignment between the nucleic acid detection data of the confirmed
cases of the cancer and human genome big data; S3 Conducting
sequence amplification and sequence alignment with each SNV site of
the SNV group as a core to screen out candidate probes of the SNV
sites and construct a candidate probe group; S4 Verifying and
confirming the probes by preparing a test chip by using sequence
information of the candidate probes of the candidate probe group,
then screening out the candidate probes that their positive
detection results are consistent with the confirmed cancer cases,
which are the gene probes capable of being used for cancer
screening.
2. The optimal selection method of gene chip probes for cancer
screening as claimed in claim 1, characterized in that the gene
chip probes capable of being used for a cancer screening are
obtained through three stages of constructing a SNV group,
constructing a candidate probe group, and verifying and confirming
the probes.
3. The optimal selection method of gene chip probes for cancer
screening as claimed in claim 1, characterized in that the SNV
sites and corresponding functional annotations of the SNV sites are
obtained by conducting sequence alignment between the nucleic acid
detection data of confirmed cancer cases of a cancer and the human
genome big data.
4. The optimal selection method of gene chip probes for cancer
screening as claimed in claim 3, characterized in that the
functional annotations of the SNV sites include functional
annotations of the genes where the SNV sites are located and
functional annotations of the chromosome segments where the SNV
sites are located.
5. The optimal selection method of gene chip probes for cancer
screening as claimed in claim 1, characterized in that the
candidate probes of the SNV sites which are capable of being used
for cancer screening and detecting are obtained through the
combination of sequence proliferation and sequence alignment with
the SNV sites as cores.
6. The optimal selection method of gene chip probes for candidate
probes screening as claimed in claim 5, characterized in that the
candidate probes have a length of 15-25 nucleotides and the number
of base pairings is 5-10 for the longest base pairings in
succession between the candidate probes and the genome sequence
other than the genome sequence itself.
7. The optimal selection method of gene chip probes for cancer
screening as claimed in claim 1, characterized in that a validation
criterion for verifying the probes is a confirmed diagnosis result
of the cancer by a hospital.
8. The optimal selection method of gene chip probes for cancer
screening as claimed in claim 1, characterized in that it is
preferred to use the sequencing data of single cells to conduct
selection of the gene chip probes for cancer screening.
9. The optimal selection method of gene chip probes for cancer
screening as claimed in claim 8, characterized in that the
sequencing data of single cells may come from but is not limited to
a cancer patient's urine exfoliated cells, menstrual blood cells,
cells got by puncturing, exfoliated cells from different parts of
the body, blood or tissue fluid.
Description
STATEMENT REGARDING SEQUENCE LISTING
[0001] The Sequence Listing associated with this application is
part of the application and is provided in text in the form of an
ASCII text file in lieu of a paper copy, and is hereby incorporated
by reference into the specification. The name of the Sequence
listing is --SEQUENCE LISTING.txt.--The text file is 824 bytes in
size, was created on Apr. 1, 2022, and is being electronically
submitted via EFS-Web.
FIELD OF THE INVENTION
[0002] The invention relates to biochip field, especially to an
optimal selection method of gene chip probes for cancer
screening.
DESCRIPTION OF THE BACKGROUND ART
[0003] Biochip technology has been widely used in many fields, such
as clinical disease diagnosis, health management, drug research and
development, animal and plant quarantine, food detection,
environmental monitoring, scientific research, forensic detection.
Biochip shows a considerable promise and great market demand.
[0004] Gene chip is a kind of biochip. It is prepared by planting a
series of probes of known sequences on a substrate of a chip. It
can be used for hybridization detection of specifically labeled
nucleic acids. It can report the nucleic acid information in the
detection object through identification, detection and information
processing.
[0005] The key technology of gene chip manufacturing is how to
effectively obtain specific probes of a gene chip. Only by
obtaining the specific probes can we design and produce gene chips.
The technology of obtaining gene chip probes has become a core of
competition in the field of gene chip industry.
[0006] At present, the technology for designing and optimizing gene
chip probes is mainly in the hands of several large foreign
companies, and a series of cancer drug screening chips have been
developed. However, there is no cancer screening gene chips for
Chinese population in the market, and developing such chips will
not only be a great contribution to the protection of national gene
resources, but is also a great challenge to the development of gene
chip technology in China. We must establish our own manufacturing
line of cancer screening gene chips, while designing gene chip
probes is a top priority.
SUMMARY OF THE INVENTION
[0007] In order to solve the shortcomings of the prior art, the
invention provides an optimal selection method of obtaining gene
chip probes for cancer screening through three stages of
constructing a point mutation site (SNV) group, constructing a
candidate probe group and verifying and confirming probes. The
optimized gene chip probes may be used for preparing gene chip on
cancer screening.
[0008] The concept of the invention is that cancer is caused by
incontrollable proliferation of cells, wherein cells proliferation
roots directly in DNA and DNA is the fundamental cause. There are
sequence changes of DNAs in the nucleic acid detection data of
confirmed cancer cases, therefore, a gene chip could be prepared to
screen cancer if specific probes for cancer is screened out and
obtained, and then making it possible to effectively prevent cancer
deterioration by interventions in the early development stages of
the cancer.
[0009] In order to solve the above problems, the invention provides
a technical solution called an optimal selection method of gene
chip probes for cancer screening comprising the following
steps:
[0010] S1 Selecting a cancer as the screening target and obtaining
nucleic acid detection data of confirmed cases of the cancer;
[0011] S2 Determining corresponding SNV sites and constructing a
SNV group by sequence alignment between the nucleic acid detection
data of the confirmed cases of the cancer and human genome big
data;
[0012] S3 Conducting sequence amplification and sequence alignment
with each SNV site of the SNV group as a core to screen out
candidate probes of the SNV sites and construct a candidate probe
group;
[0013] S4 Verifying and confirming the probes by preparing a test
chip by using sequence information of the candidate probes of the
candidate probe group, then screening out the candidate probes that
their positive detection results are consistent with the confirmed
cancer cases, which are the gene probes capable of being used for
cancer screening.
[0014] Preferably, the gene chip probes are obtained through three
stages of constructing a SNV group, constructing a candidate probe
group, and verifying and confirming probes.
[0015] Preferably, the SNV sites and corresponding functional
annotations of the SNV sites are obtained by sequence alignment
between the nucleic acid detection data of the confirmed cases of
the cancer and human genome big data.
[0016] Preferably, the functional annotations of the SNV sites
include functional annotations of genes where the SNV sites are
located and the functional annotations of the chromosome segments
where the SNV sites are located.
[0017] Preferably, the candidate probes are obtained through the
combination of sequence proliferation and sequence alignment with
the SNV sites as a core.
[0018] Preferably, the candidate probes have a length of 15-25
nucleotides and the number of base pairings is 5-10 for the longest
base pairings in succession between the candidate probes and the
genome sequence other than the genome sequence itself.
[0019] Preferably, a validation criterion for verifying the probes
is a confirmed diagnosis result of the cancer by a hospital.
[0020] Preferably, the sequencing data of single cells is used to
conduct selection of the gene chip probes for cancer screening, and
the sequencing data of single cells may come from but is not
limited to the urine exfoliated cells, menstrual blood cells, cells
got by puncturing, exfoliated cells from different parts of the
body, blood or tissue fluid from a cancer patient.
[0021] The invention has more merits than the prior art including
the established three tightly connected stages of constructing a
SNV group, constructing a candidate probe group and verifying and
confirming probes, which make us capable of correlating a specific
gene chip probes with specific cancer screening, and eventually
make it possible to screen out cancers in the early stages and to
further reduce the progress of cancer by early intervention.
DETAILED DESCRIPTION OF THE INVENTION
[0022] The invention will be further explained in details by the
following embodiments. The following embodiments are only
description instead of defining, and shall not be used to define
the protection scope of the invention. All chemical reagents and
apparatus used in the embodiments can be commercially purchased
unless otherwise specified.
Embodiment 1: An Optimal Selection Method of Gene Chip Probes for
Breast Cancer Screening
[0023] Development of gene chip probes for screening breast cancer
was conducted by cooperation with a cancer hospital (First-class
Hospital at Grade 3) or an oncology department, wherein whole
genome sequencing was made on the faulty tissues of the confirmed
breast cancer patients to obtain the nucleic acid detection data of
the breast cancerous tissues (cells).
[0024] As sequence alignment between the nucleic acid detection
data of the breast cancerous tissues (cells) and human genome
database (e.g., NCBI-GeneBank and etc.) was made together with
reference to SNV database (e.g., NCBI-Clinvar and etc.),
corresponding SNV sites of the breast cancerous tissues (cells)
were identified. For example, a SNV mutation in base conversion of
G>A was found in the nucleic acid detection data of the breast
cancerous tissues (cells), the same SNV mutation was also found in
the database of NCBI-Clinvar (rs786205165,
NM_004958.4:c.4448G>A, functional annotation
(>ref|NM_004958.4|:4419-4465Homo sapiens mechanistic target of
rapamycin kinase (MTOR), transcript variant 1, mRNA). The
functional annotation explained that the occurrence of the base
conversion made the alteration of cysteine into tyrosine in
protein. All the detected SNV sites were gathered to form the SNV
group.
[0025] Taking each SNV site in the SNV group as the core, those
sequences of 15-20 nucleotides in length were captured for sequence
alignment between the human genome database and the nucleic acid
detection data of breast cancerous tissues (cells) to screen out
sequences that have 5-10 base pairings in succession as candidate
probes; and the candidate probe group was established by gathering
all the candidate probes; wherein comprising the candidate probe
based on SNV mutation (rs786205165):
TABLE-US-00001 GAGAGCTGGAGATCCAG.
[0026] The candidate probes in the candidate probe group were
compared and analyzed by taking advantage of the nucleic acid
detection data of the breast cancerous tissues (cells) of the
confirmed cases, which was called probes verification; the breast
cancer probes capable of preparing gene chips could be selected
from the candidate probe group by verifying the probes; wherein
comprising the SNV mutation (rs786205165) probe:
GAGAGCTGGAGATCCAG.
Embodiment 2: An Optimal Selection Method of Gene Chip Probes for
Lung Cancer Screening
[0027] Development of gene chip probes for screening lung cancer
was conducted by cooperation with a cancer hospital (First-class
Hospital at Grade 3) or an oncology department, whole genome
sequencing was made on the faulty tissues of confirmed lung cancer
patients to obtain the nucleic acid detection data of the lung
cancer tissues (cells).
[0028] As sequence alignment between the nucleic acid detection
data of the lung cancer (cells) and human genome database (e.g.,
NCBI-GeneBank and etc.) was made together with reference to SNV
database (e.g., NCBI-Clinvar and etc.), corresponding SNVs of the
lung cancer (cells) were identified. For example, a SNV of deletion
mutation was found in the nucleic acid detection data of the lung
cancerous tissues (cells), the same SNV mutation was also found in
the database of NCBI-Clinvar (rs587779846,
NM_001351834.2:c.5290del, (Homo sapiens ATM serine/threonine kinase
(ATM),transcript variant1,mRNA). Functional annotations explained
that the occurrence of the base deletion led to the result that
only truncated protein was produced in the protein translation,
which further impacted the activation of regulatory proteins
including p53 and BRCA1, resulting in the occurrence of a cancer.
All the detected SNVs were gathered to form the SNV group.
[0029] Taking each SNV site in the SNV group as the core, those
sequences of 15-20 nucleotides in length were captured for sequence
alignment between the human genome database and the nucleic acid
detection data of lung cancerous tissues (cells) to screen out
sequences that have 5-10 base pairings in succession as candidate
probes. Then a candidate probe group was established by gathering
all the candidate probes, wherein comprising the candidate probe
based on SNV site (r5587779846): gctggcctattacagcctt.
[0030] The candidate probes in the candidate probe group were
compared and analyzed by taking advantage of the nucleic acid
detection data of the lung cancerous tissues (cells) of the
confirmed cases, which was called probes verification; the lung
cancer probes capable of preparing gene chips could be selected
from the candidate probe group through the probe verification,
wherein comprising the SNV (rs587779846) probe:
gctggcctattacagcctt.
[0031] The abovementioned embodiments are only preferred
embodiments of the invention; however, the protection scope of the
invention shall not be limited by the embodiments, all equivalent
replacements or modifications made according to the technical
solutions or conceptions of the invention by any person skilled in
the art within the technical range disclosed by the invention,
shall be covered by the protection of the invention.
Sequence CWU 1
1
4117DNAHomo sapiens 1gagagctgga gatccag 17217DNAHomo sapiens
2gagagctgga gatccag 17319DNAHomo sapiens 3gctggcctat tacagcctt
19419DNAHomo sapiens 4gctggcctat tacagcctt 19
* * * * *